The French team questioned the presence of a second battery in the boot of the Polo R WRCs, but the event stewards decided at close to 1am local time to declare the protest unfounded.
The case centred on Article 255A of the FIA Sporting Code, which precludes a competing car from running with two batteries.
The stewards found in favour of Volkswagen after the German team pointed to another ruling (Article 252 - 7.3) which allows a spare battery to be run in the car as a spare part.
The stewards' decision stated: "They [Volkswagen] explained that while the battery is installed in the right-rear corner of the car, it is not connected and can only be connected after disconnecting the battery in use. They also claimed that they had clarified the use of a spare battery with the FIA Technical Delegate last year and therefore used this installed battery.
"The stewards then heard the FIA technical delegate as a witness, who confirmed he had been asked by Citroen to look at the spare battery installation of cars seven and eight in parc ferme.
"He also confirmed that he has clarified with Volkswagen that this spare battery was in conformity with Article 255A and it was considered to be a spare part, He produced pictures of the spare battery showing that it was installed and not connected."
After concluding only one battery was in use and one must be disconnected before the spare could be connected and that no regulations had been broken, the stewards found in favour of Volkswagen.
Having spent much of the evening awaiting the decision, Volkswagen took the unprecedented step of communicating the stewards' announcement.
The Volkswagen press release said: "The Citroen Total Abu Dhabi Team launched a protest against the classification of the three Volkswagen Polo R WRCs. This protest was rejected due to a formal error.
"The manufacturer then filed a further two protests against Volkswagen Motorsport and Volkswagen Motorsport II (Andreas Mikkelsen's car). These protests also exhibited mistakes in their content, but were accepted by the sports commissioners. Both sides were summoned to a hearing to explain their viewpoints.
"The protests were directed at batteries, which, exclusively during parc ferme periods, are left in the cars overnight as spare parts and are then removed the following morning before leaving the service park. This has been common practice in the FIA World Rally Championship (WRC) for years.
"A technical delegate of the FIA approved this procedure prior to the 2013 season, upon explicit inquiry from Volkswagen.
"After extensive consultation, the sports commissioners dismissed the protests as unsubstantiated."
Citroen will not appeal the decision.